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Title :   CRYSTAL STRUCTURE OF RNASE III FROM AQUIFEX AEOLICUS COMPLEXED WITH DOUBLE-STRANDED RNA AT 2.5-ANGSTROM RESOLUTION

Authors :   J. Gan, J. E. Tropea, B. P. Austin, D. L. Court, D. S. Waugh, X. Ji

Date :   25 Feb 05 (Deposition) - 22 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Ribonuclease Iii, Double-Stranded Rna, Rna Interference, Endonucleolytic Cleavage, Hydrolase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Gan, J. E. Tropea, B. P. Austin, D. L. Court, D. S. Waugh, X. Ji
Intermediate States Of Ribonuclease Iii In Complex With Double-Stranded Rna
Structure V. 13 1435 2005
PubMed-ID: 16216575 | Reference-DOI: 10.1016/J.STR.2005.06.014
(for further references see the PDB file header)

*Molecule 1 - 5'-R(CPGPCPGPAPAPUPUPCPGPCPG)-3'*
	Chains	:	C, D, E, F
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - RIBONUCLEASE III
	Chains	:	A, B
	EC Number	:	3.1.26.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHPK1409
	Expression System Strain	:	BL21(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RNC
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	RNASE III

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	G E:4 , A E:5 , HOH E:118 , HOH E:177	BINDING SITE FOR RESIDUE TRS E 201

(no "SS Bond" information available for 1YYK)

(no "Cis Peptide Bond" information available for 1YYK)

(no "SAP(SNP)/Variant" information available for 1YYK)

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_3_2	PS50142	Ribonuclease III family domain profile.	RNC_AQUAE	4-121	2	A:4-121 B:4-121
2	RNASE_3_1	PS00517	Ribonuclease III family signature.	RNC_AQUAE	37-45	2	A:37-45 B:37-45
3	DS_RBD	PS50137	Double stranded RNA-binding domain (dsRBD) profile.	RNC_AQUAE	151-219	2	A:151-219 B:151-219

(no "Exon" information available for 1YYK)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:221
 aligned with RNC_AQUAE | O67082 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 
            RNC_AQUAE     1 MKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEESE 221
               SCOP domains d1yyka1 A:1-150 RNase III endonuclease catalytic domain                                                                                               d1yyka2 A:151-221 RNase III, C-terminal domain                          SCOP domains
               CATH domains 1yykA01 A:1-149  [code=1.10.1520.10, no name defined]                                                                                                1yykA02 A:150-221  [code=3.30.160.20, no name defined]                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh....hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh....eeeeeeee......eeeeeeee..eeeeeee.hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---RNASE_3_2  PDB: A:4-121 UniProt: 4-121                                                                                -----------------------------DS_RBD  PDB: A:151-219 UniProt: 151-219                              -- PROSITE (1)
                PROSITE (2) ------------------------------------RNASE_3_1-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yyk A   1 MKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEESE 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain B from PDB  Type:PROTEIN  Length:221
 aligned with RNC_AQUAE | O67082 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 
            RNC_AQUAE     1 MKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEESE 221
               SCOP domains d1yykb1 B:1-150 RNase III endonuclease catalytic domain                                                                                               d1yykb2 B:151-221 RNase III, C-terminal domain                          SCOP domains
               CATH domains 1yykB01 B:1-149  [code=1.10.1520.10, no name defined]                                                                                                1yykB02 B:150-221  [code=3.30.160.20, no name defined]                   CATH domains
           Pfam domains (1) ------------------------------------Ribonuclease_3-1yykB03 B:37-121                                                      ------------------------------dsrm-1yykB01 B:152-217                                            ---- Pfam domains (1)
           Pfam domains (2) ------------------------------------Ribonuclease_3-1yykB04 B:37-121                                                      ------------------------------dsrm-1yykB02 B:152-217                                            ---- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhh....hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...eeeeeeee......eeeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---RNASE_3_2  PDB: B:4-121 UniProt: 4-121                                                                                -----------------------------DS_RBD  PDB: B:151-219 UniProt: 151-219                              -- PROSITE (1)
                PROSITE (2) ------------------------------------RNASE_3_1-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yyk B   1 MKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEESE 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain C from PDB  Type:RNA  Length:12
                                            
                 1yyk C   1 CGCGAAUUCGCG  12
                                    10

Chain D from PDB  Type:RNA  Length:12
                                            
                 1yyk D  13 CGCGAAUUCGCG  24
                                    22

Chain E from PDB  Type:RNA  Length:12
                                            
                 1yyk E   1 CGCGAAUUCGCG  12
                                    10

Chain F from PDB  Type:RNA  Length:12
                                            
                 1yyk F  13 CGCGAAUUCGCG  24
                                    22

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Double Stranded RNA Binding Domain (204)

Homologous Superfamily: [code=3.30.160.20, no name defined] (122)

[unclassified] (7)

1a	1yykA02	A:150-221
1b	1yykB02	B:150-221

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Ribonuclease iii, N-terminal Endonuclease Domain; Chain A (11)

Homologous Superfamily: [code=1.10.1520.10, no name defined] (11)

[unclassified] (5)

2a	1yykA01	A:1-149
2b	1yykB01	B:1-149

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DSRM (45)

Family: dsrm (27)

Aquifex aeolicus (7)

1a	dsrm-1yykB01	B:152-217
1b	dsrm-1yykB02	B:152-217

Clan: no clan defined [family: Ribonuclease_3] (11)

Family: Ribonuclease_3 (11)

Aquifex aeolicus (9)

2a	Ribonuclease_3-1yykB03	B:37-121
2b	Ribonuclease_3-1yykB04	B:37-121

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (RNC_AQUAE | O67082)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003725	double-stranded RNA binding	Interacting selectively and non-covalently with double-stranded RNA.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0004525	ribonuclease III activity	Catalysis of the endonucleolytic cleavage of RNA with 5'-phosphomonoesters and 3'-OH termini; makes two staggered cuts in both strands of dsRNA, leaving a 3' overhang of 2 nt.
biological process
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0006396	RNA processing	Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0016075	rRNA catabolic process	The chemical reactions and pathways resulting in the breakdown of rRNA, ribosomal RNA, a structural constituent of ribosomes.
	GO:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	3.1.26.3
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UniProtKB/Swiss-Prot
	RNC_AQUAE \| O67082	:	1i4s 1jfz 1rc5 1rc7 1yyo 1yyw 1yz9 2ez6 2nue 2nuf 2nug 4m2z 4m30

1i4s	THE CRYSTAL STRUCTURE OF RNASE III ENDONUCLEASE DOMAIN FROM AQUIFEX AEOLICUS
1jfz	CRYSTAL STRUCTURE OF A MN(II)COMPLEX OF RNASE III ENDONUCLEASE DOMAIN FROM AQUIFEX AEOLICUS
1o0w	THE CRYSTAL STRUCTURE OF RNASE III FROM THERMOTOGA MARITIMA
1rc5	THE CRYSTAL STRUCTURE OF A MG(II) COMPLEX OF RNASE III ENDONUCLEASE DOMAIN FROM AQUIFEX AEOLICUS
1rc7	CRYSTAL STRUCTURE OF RNASE III MUTANT E110K FROM AQUIFEX AEOLICUS COMPLEXED WITH DOUBLE-STRANDED RNA
1yyo	THE SAME PROTEIN WITH MUTANT E110K
1yyw	THE SAME PROTEIN AT 2.8-ANGSTROM RESOLUTION
1yz9	THE SAME PROTEIN WITH MUTANT E110Q

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (2, 4)

Gene Ontology (14, 14)

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